Initial release of bash shell script to convert template workflow scripts to executable ones.

video_prediction_savp/env_setup/generate_workflow_scripts

+#!/usr/bin/env bash
+# **************** Description ****************
+# Converts given template workflow script (path has to be passed as first argument) to
+# an executable workflow (Batch) script.
+# Note, that this first argument has to be passed with "_template.sh" omitted!
+# A second argument can be passed to set the e-mail address.
+# On HDF-ML and Juwels, where jutil is available, this is done automatically,
+# i.e. no second argument is required.
+# Example:
+#    ./generate_workflow_scripts.sh ../HPC_scripts/generate m.mustermann@fz-juelich.de
+# **************** Description ****************
+#
+#sanity checks
+if ! [ $# -eq 1]; then
+  echo "ERROR: Pass path to workflow script to be generated..."
+else
+  curr_script = $1
+fi
+
+if ! [[ -f ${curr_script}_template.sh ]]; then
+  echo "WARNING: Could not find expected Batch script '${curr_script}_template.sh'."
+  echo "Thus, no corresponding executable script is created!"
+  exit 0              # still ok, i.e. only a WARNING is raised
+fi
+# create copy of template which is modified subsequenty
+cp ${curr_script}_template.sh ${curr_script}_op.sh
+# remove template identifiers
+num_lines=`awk '/Template identifiers/{ print NR }'
+line_s=`echo ${num_lines} | cut -d' ' -f 1`
+line_e=`echo ${num_lines} | cut -d' ' -f 2`
+if [[ ${line_s} == "" || ${line_e} == "" ]]; then
+  echo "ERROR: ${curr_script}_template.sh exists, but does not seem to be a valid template script."
+  exit 1
+else
+  sed -e '${line_s},${line_e}d' ${curr_script}_op.sh
+fi
+
+# set correct e-mail address if possible, otherwise remove
+if ! [ -z "$2" ]; then
+  USER_EMAIL=$2
+else
+  if [ command -v jutil ]; then
+    USER_EMAIL=$(jutil user show -o json | grep email | cut -f2 -d':' | cut -f1 -d',' | cut -f2 -d'"')
+  else
+    USER_MAIL=""
+  fi
+fi
+sed -i "s/--mail-user=.*/--mail-user=$USER_EMAIL/g" ${curr_script}_op.sh
+